The KEMRI Graduate School was established by KEMRI Board of Management in 1992 to train postgraduate students in health research through opportunities presented by the well-established medical research facilities and global research expertise available at KEMRI.

The goal of the Graduate School is to develop a human resource base equipped with updated research skills and knowledge to provide solutions to the rapidly growing health care delivery challenges facing Kenya and the Africa region.

In 2003, The School entered into partnership with Jomo Kenyatta University of Agriculture and Technology (JKUAT) to offer Masters and PhD degrees in infectious diseases and tropical medicine. As of December, 2017, more than 400 Masters and 70 PhD students had graduated from the KEMRI-JKUAT collaboration.

In 2018, The Graduate School began the process with Kenya Commission of University Education (CUE) to obtain her own university charter as a specialized degree awarding arm of The Kenya Medical Research Institute.